How can I substract two FILETIMEs?

Read the documentation of FILETIME:

It is not recommended that you add and subtract values from the FILETIME structure to obtain relative times. Instead, you should copy the low- and high-order parts of the file time to a ULARGE_INTEGER structure, perform 64-bit arithmetic on the QuadPart member, and copy the LowPart and HighPart members into the FILETIME structure.

And there you have your single number, too (QuadPart of the ULARGE_INTEGER structure).